A Revised Root for the Human Y Chromosome Differentiation and Diversity Landscape Among North African Populations

Journal of Investigative Genomics

Book Review Open Access A revised root for the human Y chromosome differentiation and diversity landscape among North African populations

Abstract Volume 5 Issue 1 - 2018 North Africa is a crucial area in the settlement history of modern humans because K Bentayebi, A Hajitou it represents a possible connection between Africa and Europe. So far, genetic data were inconclusive about the fact that this region constitutes a barrier to gene flow, Department of Medicine, Imperial College London, UK as previous results were highly variable depending on the genetic locus studied. The Correspondence: Kaoutar Bentayebi, Phage Therapy Group, present study evaluates the impact of North Africa in reducing gene flow between Division of Brain Sciences, Department of Medicine, Imperial populations from Africa and Europe, by comparing formally various genetic loci in the College London, Hammersmith Hospital Campus, London W12 Y chromosome and analyzing several parameters of population differentiation taking 0NN, UK, Tel +07388288672, into account the effects of both demography and natural selection at some loci. The Email [email protected] Y chromosome is inherited through the paternal line and remains virtually unchanged through many generations. The combination of the analysis of Y chromosome STR Received: June 16, 2017 | Published: September 07, 2018 and SNP will allow the analysis of human evolution in paternal lineages in different time scales. The forensic implication of the results are discussed.

Keywords: North Africa, Y chromosome, STR, SNP, ancestry, population, gene flow

Introduction record of the history of human males, and of the relationships between past populations. A number of recent studies carried out in the The Y chromosome has a curious role in population Genetics Moroccan, Algerian and Tunisian populations have shown that most Y and forensic genetics. It is male specific and constitutively haploid. chromosomes can be classified into monophyletic units (haplogroups), It passes from father to son, and, unlike other chromosomes, largely which tend to be specific to each continent and major ethnic group.4–6 escapes meiotic recombination. Two segments (the pseudoautosomal This study takes advantage of this ethnic/geographic specificity to regions) do recombine with the X, but this amount to less than 3 Mb of define better the origins and relationships of the populations living in 1 its ~60-Mb length, which makes it easier to study than the autosomes. the Western Mediterranean basin. These traits, explains its use in an increasing number of studies, especially those that address the history of the human population We are interested in using two types of YDNA markers in and makes it easier to study than the autosomes. Nevertheless, the our study: STR and SNP. Applications of these markers include Y chromosome continues to be overshadowed in these studies by the phylogeny, forensics, paternity tests, genetic marker for disease, gene autosomal chromosome and mtDNA, despite containing far more mapping, selection of traits in breeding, etc. i) STR stands for “short genetic information than either. One reason for the lagging position of tandem repeat”. The STRs are repetitions of 2 or more nucleotides the Y chromosome has been a delay in the generation of useful data. that occur mostly in the non-coding parts of the DNA. The number The first PHYLOGENETIC TREE for human mtDNA was published of repeats is called allele value. STRs are highly polymorphic which in 1987,2 and the first for the Y chromosome was published in 1989.3 means that the amount of repetitions in a specific STR can be different Since then, Y-chromosome-based studies have slowly accumulated; from person to person. The same number of repeats between persons with the maturation of sequencing and genotyping technologies, a across a wide range of STR markers indicates that they are most likely tremendous increase in all kinds of genetic data looms. It is therefore related. ii) SNP stands for “single nucleotide polymorphism”. This an appropriate time to reflect on what the Y chromosome can offer to means that there is a variation or mutation in one single nucleotide population-genetic studies. at a specific location in the genome (either in a gene or in anon- coding region). Unlike Y-STR markers which can have multiple Overview on Y chromosome in Noth Africa repeats, SNP markers often only exist in 2 forms – the ancestral and the mutated allele. Y chromosome-specific single nucleotide The western Mediterranean region has a wide genetic interest in polymorphisms (SNPs) are particularly useful for identification population genetics and forensic genetic studies. It has been a focus of stable paternal lineages because of their low rate of parallel and of genetic research for many years, due to its geostrategic position back mutations. By testing highly polymorphic Y-STR markers that distinguished by its ancient and shifting history. The sequence can inform of recent ancestry in addition to the Y-SNP markers an differentiation of human Y chromosomes has occurred during and even more detailed DNA profile can be obtained.7–9 Data here were after the process of colonization and diffusion into the different collected from previous analysis on three North African populations geographic regions and continents, and its dissection is a useful tool (Morocco, Algeria and Tunisia). Y chromosomes were typed using 17 for the investigation of range expansions, migrations and other forms Short Tandem Repeats polymorphisms and SNP polymorphism for 52 of gene flow in prehistoric and historic times. In other words, the Tunisian,10 102 Algerian11 and 267 Moroccan.12,13 All 421 individuals sequence variation of modern Y chromosomes represents a unique

Submit Manuscript | http://medcraveonline.com J Investig Genomics. 2018;5(1):35‒37. 35 © 2018 Bentayebi et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and build upon your work non-commercially. Copyright: A revised root for the human Y chromosome differentiation and diversity landscape among North African 36 populations ©2018 Bentayebi et al.

were tested for seventeen STRs (DYS19, DYS385 a/b, DYS389 I/II, near Gorom-Gorom, in Burkina Faso, and 81.8% from Gosi in Mali. DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, There was a much lower frequency of 11.1% in the vicinity of Tanut in DYS448, DYS456, DYS458, DYS635 (Y GATA C4), and YGATA the Republic of Niger. E-M81 is also quite common among North H4. dinucleotide repeat markers (YCAIIa, YCAIIb, DYS413a, and African Arabic-speaking groups. It is generally found at frequencies DYS413b). around 45% in coastal cities of the Maghreb (Oran, Tunis, Tizi Ouzou, Algiers).11,16 It is also seen, although at low frequency, in From the extreme north western Africa to the east, data showed a the Iberian Peninsula (4%) and Sicily (3%) due to recent gene flow decreasing pattern of diversity. The Moroccan, Algerian and Tunisian from Northwest Africa through Gibraltar strait.20,21 The second most populations showed the respective values of different haplotypes: 257 abundant haplogroup in the studied population was J1 that showed (96.25%), 93 (91.18%) and 39 (75%) of which 247, 88 and 29 were a decreasing prevalence from Tunisia to Morocco with respectively, unique. Forensic parameters displayed in table 1 showed a striking 35%, 22.5% and 10%. The J1 haplogroup, defined by the single difference in discrimination capacity among the three North African nucleotide polymorphism (SNP) M267, is most frequent in the Arabian populations for the 17 Y-STR markers, with a low value in Tunisia Peninsula especially in Yemen (76%).22 This could be attributed to the (0,750) compared to Algeria (0.918) and Morocco (0.963). Generally, early medieval period during which the Semitic expansion spread J1 lower levels or variation are observed on the Y chromosome in out of Arabia into North Africa (Figure 1).23 the Tunisian population. The smaller sample size of the Tunisian population included in this study could have affected the results and lead to show a lower diversity within this population. We couldn’t increase de sample size because we didn’t find studies in the literature describing wider Tunisian population sample. Further analysis on this population including these markers has to be done. The increasing pattern of genetic diversity from the North eastern part of Maghreb to the western shores, may be seemingly be explained by the out of Africa model. Indeed, the genetic segments of Y chromosome mighthad further time interval to acquire genetic differences and variation in Morocco compared to Tunisia. Two microvariant alleles (18.2 and 19.2) were observed at the locus DYS458 in the three studied populations, with a lower frequency than that observed in the Upper (Southern) Egyptian population. Although there are data suggesting that locus DYS458 may be affected by a higher mutation Figure 1 Distribution and movement of the major E-M215 lineage. rate compared to other tetrameric Y-STR loci,14 the observed E-M215 also known as E1b1b was dated by Cruciani in 2007 to about 22,400 microvariants seem to reflect a single mutational event (Table 1). years ago in the Horn of Africa. E-M215 is defined as one of the major patriline ages of humanity, supporting the “out of Africa” theory. Recent Table 1 Statistical parameters of 17 Y-chromosomal short tandem repeat discovery showed that the earliest homo sapiens was found in Morocco loci in 421 North African male samples and has about 300.000 years old. In Africa, E-M215 is distributed in highest frequencies in the Horn of Africa and North Africa, whence it has in recent Population Sample UH DH GD HD DC millennia expanded as far south as South Africa, and northwards into DYS385: Western Asia and Europe (especially the Mediterranean and the Balkans). Morocco 267 247 257 0.9991 0.963 0.887 Studies on Y chromosome showed that EM81 is the most frequent lineage in North Africa. E-M78 is more present in the east and decline toward the west DYS458: Algeria 102 88 93 0.997 0.918 in contrast with E-M81.6,24–28 0.806 Tunisia 52 29 39 - - 0.750 Discussion *Abbreviations: UH, unique haplotype; DH, different haplotype; GD, gene The analysis of a large panel of Y-STR and Y-SNP are very useful diversity; HD, haplotype diversity; DC, discrimination capacity. in population genetics to characterize the male lineage of human In order to get a deeper insight on the Y chromosome diversity in populations and constitute a benefic tool to forensic expert. The the Maghreb region, 41 Y-SNP were analyzed in a Tunisian population, previous studies showed that the genetic background of Maghrebien and 22 biallelic markers respectively in Algeria and Morocco. The populations is very similar and close each other. The genetic diversity haplogroup E-M81, formally, E1b1b1b, E3b1b and E3b2 was the has an increasing pattern from East to west of North Africa, seemingly major Y chromosome haplogroup abundantly and respectively found supporting the hypothesis of out of Africa model. Most results showed in Morocco, Tunisia and Algeria. This haplogroupis the most common that the Maghrib is characterized by the predominance of the EM-81 Y chromosome haplogroup in the Maghreb, dominated by its sub- haplogroup that is specific and native to this region. Its presence in clade E-M183. It is thought to have originated in the area of North some region of southern Europe may be due to the colonization of North Africa 5,600 years ago.15,16 This haplogroup reaches a mean frequency African Arabic and berbers to the Iberian Peninsula through the strait of 42% in North Africa, decreasing in frequency from approximately of Gibraltar. The forensic values encourage widely the use of these 80% or more in some Moroccan Berber populations, including markers in forensic genetics to resolve some complex kinship cases. Saharaw is, to approximately 10% to the east of this range in Egypt.16–18 Also, haplotype can help the investigators to infer the provenience of Because of its prevalence among these groups and also others such the subject who left the evidence. At the same time, information on as Mozabite, Middle Atlas, Kabyle and other Berber groups, it is the geographic and ethnic distribution of Y-SNP haplogroups and their sometimes referred to as a genetic “Berber marker”. Pereira et al.,19 internal YSTR variability can assist the expert with the estimate of the report high levels amongst Tuareg in two Saharan populations - 77.8% frequency of a particular haplotype in populations for which a specific

Citation: Bentayebi K, Hajitou A. A revised root for the human Y chromosome differentiation and diversity landscape among North African populations. J Investig Genomics. 2018;5(1):35‒37. DOI: 10.15406/jig.2018.05.00075 Copyright: A revised root for the human Y chromosome differentiation and diversity landscape among North African 37 populations ©2018 Bentayebi et al.

reference database of Y-STR haplotypes isnot yet available. This study of the AmpFlSTRYfiler PCR amplification kit: a male specific, confirmed that precious informations might come both from YSNPs singleamplification 17 Y-STR multiplex system. J Forensic Sci. haplogroup distribution and microsatellite variability to characterize 2006;51(1):64–75. the genetic background of the North West African population. 15. Cruciani F, La Fratta R, Santolamazza P, et al. Phylogeographic analysis of haplogroup E3b (E-M215) Y chromosomes reveals multiple migratory Acknowledgements events within and out of Africa. Am J Hum Genet. 2004;74:1014–1022.

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